[mira_talk] Re: 454 mapping
- From: davis gimode <dgimode@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 10 May 2012 10:59:10 +0300
Previously I was using v 3.0.4 of Mira on a 32 bit machine, now ive
tried it on a 64bit machine with v3.4. When I run the command with the
suggested modifications, this is what i get:
Loading backbone from FASTA file: indica_backbone_in.fasta (quality:
indica_backbone_in.fasta.qual)
Could not find FASTA quality file indica_backbone_in.fasta.qual, using
default values for these reads.
Localtime: Tue May 8 12:38:17 2012
Counting sequences in FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
Found 66338 sequences.
Localtime: Tue May 8 12:38:24 2012
Loading data from FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
Localtime: Tue May 8 12:40:15 2012
rnm size: 0
No FASTA quality file given, using default qualities for all reads just loaded.
Localtime: Tue May 8 12:40:37 2012
Done.
Loaded 66338 reads with 89026397 raw bases.
0 reads have quality accounted for.
Localtime: Tue May 8 12:40:37 2012
Generated 0 unique strain ids for 66338 reads.
Killed
I dont know how to make it work. And is there a way to specify for the
454 sequences that should be assembled on to the backbone.?
Thanks.
On Sun, May 6, 2012 at 8:57 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On 05/03/2012 01:22 PM, davis gimode wrote:
>>
>> I am trying to do a mapping assembly of 454 data on to a reference
>> genome. My call parameters are:
>>
>> mira --project=indica --job=mapping,genome,accurate,454 -AS:nop=4
>>
>> -SB:load_backbone=yes:startbackboneusage_inpass=3:backbone_strainname=indica_backbone_in.fasta:backbone_filetype=fasta:bbq=-1
>>
>> However, it requires quality scores for the backbone i.e it wants
>> indica_backbone_in.fasta.qual which i dont have. How do i disable mira
>> from requiring the quality files?
>
>
> Well, MIRA will load a quality file if present, but won't stop (at least it
> should not).
>
> Which version of MIRA are you using? In 3.4.0, MIRA loads the FASTA, sees
> that there's no quality file and just trots along. Here's the relevant part
> of the log output:
>
> ------------------------ snip -----------------------------------
> Localtime: Sun May 6 19:46:46 2012
>
> Loading backbone from FASTA file: indica_backbone_in.fasta (quality:
> indica_backbone_in.fasta.qual)
> Could not find FASTA quality file indica_backbone_in.fasta.qual, using
> default values for these reads.
> Localtime: Sun May 6 19:46:46 2012
> Counting sequences in FASTA file:
> ------------------------ snip -----------------------------------
>
> By the way: your contains two errors and a minor problem:
> 1) (minor) -SB:sbuip is used only for combined mapping/de-novo assemblies.
> You do not do that here, so it's useless to state it.
> 2) -SB:bsn is the name of your backbone organism, not the name of a file.
> I.e., change
> -SB:bsn=indica_backbone_in.fasta
> to something like
> -SB:bsn=IThinkThatStrainIsAnIndicaOrWhateverYouWantToNameThatThing
>
> 3) -SB:bbq should be set independently of read qualities. Using bbq=-1 is
> usefull only for very special borderline cases. Go with a quality of "30":
> -SB:bbq=30
>
> B.
>
>
>
> --
> You have received this mail because you are subscribed to the mira_talk
> mailing list. For information on how to subscribe or unsubscribe, please
> visit http://www.chevreux.org/mira_mailinglists.html
--
Davis M. Gimode
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
